Starting phenix.real_space_refine
on Mon Nov 18 06:21:30 2024 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss5_40744/11_2024/8ss5_40744.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss5_40744/11_2024/8ss5_40744.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.56
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss5_40744/11_2024/8ss5_40744.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss5_40744/11_2024/8ss5_40744.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss5_40744/11_2024/8ss5_40744.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss5_40744/11_2024/8ss5_40744.cif"
  }
  resolution = 3.56
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.005 sd=   0.075
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S     104      5.16       5
     Na      1      4.78       5
     C   10182      2.51       5
     N    2524      2.21       5
     O    2826      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 36 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib"
  Total number of atoms: 15637
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 595, 4662
          Classifications: {'peptide': 595}
          Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 577}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 3156
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 404, 3156
          Classifications: {'peptide': 404}
          Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 390}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' NA': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    C, D
  Time building chain proxies: 13.15, per 1000 atoms: 0.84
  Number of scatterers: 15637
  At special positions: 0
  Unit cell: (120.84, 124.02, 135.68, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S     104     16.00
     Na      1     11.00
     O    2826      8.00
     N    2524      7.00
     C   10182      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 718 " - pdb=" SG  CYS A 773 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 890 " - pdb=" SG  CYS A 900 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 718 " - pdb=" SG  CYS B 773 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.76
  Conformation dependent library (CDL) restraints added in 2.0 seconds
  

  3932 Ramachandran restraints generated.
    1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3656

  Finding SS restraints...
    Secondary structure from input PDB file:
      70 helices and 22 sheets defined
      54.0% alpha, 5.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.46
  Creating SS restraints...
    Processing helix  chain 'A' and resid 423 through 437
      removed outlier: 3.724A  pdb=" N   LYS A 434 " --> pdb=" O   ALA A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 462 through 469
      removed outlier: 3.632A  pdb=" N   TYR A 469 " --> pdb=" O   GLY A 465 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 482 through 487
      removed outlier: 3.502A  pdb=" N   GLU A 486 " --> pdb=" O   THR A 482 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 522 through 546
      removed outlier: 3.509A  pdb=" N   VAL A 530 " --> pdb=" O   TRP A 526 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   SER A 544 " --> pdb=" O   LEU A 540 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   ARG A 545 " --> pdb=" O   PHE A 541 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 572 through 585
      removed outlier: 3.886A  pdb=" N   TRP A 578 " --> pdb=" O   PHE A 574 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   MET A 585 " --> pdb=" O   LEU A 581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 595 through 630
      removed outlier: 3.668A  pdb=" N   ILE A 600 " --> pdb=" O   LEU A 596 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   VAL A 601 " --> pdb=" O   SER A 597 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   GLY A 602 " --> pdb=" O   GLY A 598 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   TRP A 606 " --> pdb=" O   GLY A 602 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   PHE A 607 " --> pdb=" O   GLY A 603 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   LEU A 610 " --> pdb=" O   TRP A 606 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ILE A 611 " --> pdb=" O   PHE A 607 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   SER A 614 " --> pdb=" O   LEU A 610 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   ALA A 618 " --> pdb=" O   SER A 614 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   THR A 625 " --> pdb=" O   ALA A 621 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   VAL A 626 " --> pdb=" O   ALA A 622 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 635 through 642
      removed outlier: 3.789A  pdb=" N   LYS A 641 " --> pdb=" O   GLU A 637 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   GLN A 642 " --> pdb=" O   ASP A 638 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 653 through 661
      removed outlier: 3.873A  pdb=" N   PHE A 659 " --> pdb=" O   THR A 655 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ARG A 660 " --> pdb=" O   LYS A 656 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   ARG A 661 " --> pdb=" O   GLU A 657 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 664 through 676
    Processing helix  chain 'A' and resid 686 through 695
    Processing helix  chain 'A' and resid 706 through 714
      removed outlier: 3.865A  pdb=" N   TYR A 711 " --> pdb=" O   THR A 707 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   GLN A 714 " --> pdb=" O   GLU A 710 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 743 through 752
      removed outlier: 3.547A  pdb=" N   ASN A 747 " --> pdb=" O   GLY A 743 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   LEU A 751 " --> pdb=" O   ASN A 747 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 757 through 767
      removed outlier: 3.845A  pdb=" N   LYS A 763 " --> pdb=" O   LEU A 759 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ASN A 764 " --> pdb=" O   ASP A 760 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 793 through 822
      removed outlier: 3.524A  pdb=" N   LEU A 805 " --> pdb=" O   GLY A 801 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   LEU A 808 " --> pdb=" O   GLY A 804 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   LEU A 811 " --> pdb=" O   MET A 807 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ILE A 812 " --> pdb=" O   LEU A 808 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   PHE A 814 " --> pdb=" O   ALA A 810 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 834 through 858
      removed outlier: 3.611A  pdb=" N   LEU A 852 " --> pdb=" O   GLY A 848 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ALA A 855 " --> pdb=" O   LEU A 851 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 922 through 928
      removed outlier: 4.169A  pdb=" N   ARG A 926 " --> pdb=" O   LEU A 922 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 929 through 952
      removed outlier: 3.761A  pdb=" N   SER A 935 " --> pdb=" O   PHE A 931 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ILE A 941 " --> pdb=" O   PHE A 937 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ILE A 944 " --> pdb=" O   PHE A 940 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   ARG A 952 " --> pdb=" O   ILE A 948 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 956 through 990
      removed outlier: 3.655A  pdb=" N   PHE A 965 " --> pdb=" O   VAL A 961 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ILE A 967 " --> pdb=" O   GLY A 963 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   LEU A 968 " --> pdb=" O   ILE A 964 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   SER A 969 " --> pdb=" O   PHE A 965 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1004 through 1033
      removed outlier: 3.645A  pdb=" N   LEU A1015 " --> pdb=" O   ALA A1011 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   MET A1023 " --> pdb=" O   SER A1019 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   VAL A1025 " --> pdb=" O   GLY A1021 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 416 through 419
    Processing helix  chain 'B' and resid 423 through 436
    Processing helix  chain 'B' and resid 461 through 470
      removed outlier: 3.575A  pdb=" N   TYR B 469 " --> pdb=" O   GLY B 465 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 482 through 487
    Processing helix  chain 'B' and resid 515 through 519
      removed outlier: 3.549A  pdb=" N   LEU B 518 " --> pdb=" O   PHE B 515 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 522 through 547
      removed outlier: 3.504A  pdb=" N   MET B 527 " --> pdb=" O   TYR B 523 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   PHE B 546 " --> pdb=" O   LEU B 542 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 572 through 585
      removed outlier: 3.717A  pdb=" N   LEU B 577 " --> pdb=" O   ILE B 573 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   TRP B 578 " --> pdb=" O   PHE B 574 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   SER B 580 " --> pdb=" O   SER B 576 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   LEU B 581 " --> pdb=" O   LEU B 577 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 595 through 626
      removed outlier: 3.882A  pdb=" N   TRP B 605 " --> pdb=" O   VAL B 601 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   PHE B 608 " --> pdb=" O   VAL B 604 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   LEU B 610 " --> pdb=" O   TRP B 606 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ILE B 611 " --> pdb=" O   PHE B 607 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ILE B 612 " --> pdb=" O   PHE B 608 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   VAL B 626 " --> pdb=" O   ALA B 622 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 635 through 642
      removed outlier: 3.666A  pdb=" N   GLN B 642 " --> pdb=" O   ASP B 638 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 653 through 662
      removed outlier: 3.619A  pdb=" N   PHE B 659 " --> pdb=" O   THR B 655 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ARG B 660 " --> pdb=" O   LYS B 656 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 666 through 677
      removed outlier: 3.606A  pdb=" N   MET B 674 " --> pdb=" O   MET B 670 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   SER B 676 " --> pdb=" O   THR B 672 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 686 through 696
      removed outlier: 3.525A  pdb=" N   ALA B 691 " --> pdb=" O   ALA B 687 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 707 through 713
    Processing helix  chain 'B' and resid 742 through 757
      removed outlier: 3.534A  pdb=" N   ASN B 747 " --> pdb=" O   GLY B 743 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   LEU B 751 " --> pdb=" O   ASN B 747 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 757 through 767
    Processing helix  chain 'B' and resid 793 through 820
      removed outlier: 3.589A  pdb=" N   TYR B 797 " --> pdb=" O   ALA B 793 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   TYR B 816 " --> pdb=" O   ILE B 812 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 423 through 437
      removed outlier: 3.724A  pdb=" N   LYS C 434 " --> pdb=" O   ALA C 430 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 462 through 469
      removed outlier: 3.632A  pdb=" N   TYR C 469 " --> pdb=" O   GLY C 465 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 482 through 487
      removed outlier: 3.502A  pdb=" N   GLU C 486 " --> pdb=" O   THR C 482 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 522 through 546
      removed outlier: 3.510A  pdb=" N   VAL C 530 " --> pdb=" O   TRP C 526 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   SER C 544 " --> pdb=" O   LEU C 540 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   ARG C 545 " --> pdb=" O   PHE C 541 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 572 through 585
      removed outlier: 3.886A  pdb=" N   TRP C 578 " --> pdb=" O   PHE C 574 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   MET C 585 " --> pdb=" O   LEU C 581 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 595 through 630
      removed outlier: 3.667A  pdb=" N   ILE C 600 " --> pdb=" O   LEU C 596 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   VAL C 601 " --> pdb=" O   SER C 597 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   GLY C 602 " --> pdb=" O   GLY C 598 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   TRP C 606 " --> pdb=" O   GLY C 602 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   PHE C 607 " --> pdb=" O   GLY C 603 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   LEU C 610 " --> pdb=" O   TRP C 606 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ILE C 611 " --> pdb=" O   PHE C 607 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   SER C 614 " --> pdb=" O   LEU C 610 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   ALA C 618 " --> pdb=" O   SER C 614 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   THR C 625 " --> pdb=" O   ALA C 621 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   VAL C 626 " --> pdb=" O   ALA C 622 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 635 through 642
      removed outlier: 3.789A  pdb=" N   LYS C 641 " --> pdb=" O   GLU C 637 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   GLN C 642 " --> pdb=" O   ASP C 638 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 653 through 661
      removed outlier: 3.874A  pdb=" N   PHE C 659 " --> pdb=" O   THR C 655 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ARG C 660 " --> pdb=" O   LYS C 656 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   ARG C 661 " --> pdb=" O   GLU C 657 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 664 through 676
    Processing helix  chain 'C' and resid 686 through 695
    Processing helix  chain 'C' and resid 706 through 714
      removed outlier: 3.865A  pdb=" N   TYR C 711 " --> pdb=" O   THR C 707 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   GLN C 714 " --> pdb=" O   GLU C 710 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 743 through 752
      removed outlier: 3.547A  pdb=" N   ASN C 747 " --> pdb=" O   GLY C 743 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   LEU C 751 " --> pdb=" O   ASN C 747 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 757 through 767
      removed outlier: 3.845A  pdb=" N   LYS C 763 " --> pdb=" O   LEU C 759 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ASN C 764 " --> pdb=" O   ASP C 760 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 793 through 822
      removed outlier: 3.525A  pdb=" N   LEU C 805 " --> pdb=" O   GLY C 801 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   LEU C 808 " --> pdb=" O   GLY C 804 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   LEU C 811 " --> pdb=" O   MET C 807 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ILE C 812 " --> pdb=" O   LEU C 808 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   PHE C 814 " --> pdb=" O   ALA C 810 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 834 through 858
      removed outlier: 3.610A  pdb=" N   LEU C 852 " --> pdb=" O   GLY C 848 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ALA C 855 " --> pdb=" O   LEU C 851 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 922 through 928
      removed outlier: 4.170A  pdb=" N   ARG C 926 " --> pdb=" O   LEU C 922 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 929 through 952
      removed outlier: 3.761A  pdb=" N   SER C 935 " --> pdb=" O   PHE C 931 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ILE C 941 " --> pdb=" O   PHE C 937 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ILE C 944 " --> pdb=" O   PHE C 940 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ARG C 952 " --> pdb=" O   ILE C 948 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 956 through 990
      removed outlier: 3.656A  pdb=" N   PHE C 965 " --> pdb=" O   VAL C 961 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ILE C 967 " --> pdb=" O   GLY C 963 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   LEU C 968 " --> pdb=" O   ILE C 964 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   SER C 969 " --> pdb=" O   PHE C 965 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1004 through 1033
      removed outlier: 3.644A  pdb=" N   LEU C1015 " --> pdb=" O   ALA C1011 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   MET C1023 " --> pdb=" O   SER C1019 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   VAL C1025 " --> pdb=" O   GLY C1021 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 416 through 419
    Processing helix  chain 'D' and resid 423 through 436
    Processing helix  chain 'D' and resid 461 through 470
      removed outlier: 3.575A  pdb=" N   TYR D 469 " --> pdb=" O   GLY D 465 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 482 through 487
    Processing helix  chain 'D' and resid 515 through 519
      removed outlier: 3.549A  pdb=" N   LEU D 518 " --> pdb=" O   PHE D 515 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 522 through 547
      removed outlier: 3.503A  pdb=" N   MET D 527 " --> pdb=" O   TYR D 523 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   PHE D 546 " --> pdb=" O   LEU D 542 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 572 through 585
      removed outlier: 3.718A  pdb=" N   LEU D 577 " --> pdb=" O   ILE D 573 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   TRP D 578 " --> pdb=" O   PHE D 574 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   SER D 580 " --> pdb=" O   SER D 576 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   LEU D 581 " --> pdb=" O   LEU D 577 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 595 through 626
      removed outlier: 3.883A  pdb=" N   TRP D 605 " --> pdb=" O   VAL D 601 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   PHE D 608 " --> pdb=" O   VAL D 604 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   LEU D 610 " --> pdb=" O   TRP D 606 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ILE D 611 " --> pdb=" O   PHE D 607 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ILE D 612 " --> pdb=" O   PHE D 608 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   VAL D 626 " --> pdb=" O   ALA D 622 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 635 through 642
      removed outlier: 3.666A  pdb=" N   GLN D 642 " --> pdb=" O   ASP D 638 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 653 through 662
      removed outlier: 3.619A  pdb=" N   PHE D 659 " --> pdb=" O   THR D 655 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ARG D 660 " --> pdb=" O   LYS D 656 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 666 through 677
      removed outlier: 3.605A  pdb=" N   MET D 674 " --> pdb=" O   MET D 670 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   SER D 676 " --> pdb=" O   THR D 672 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 686 through 696
      removed outlier: 3.524A  pdb=" N   ALA D 691 " --> pdb=" O   ALA D 687 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 707 through 713
    Processing helix  chain 'D' and resid 742 through 757
      removed outlier: 3.534A  pdb=" N   ASN D 747 " --> pdb=" O   GLY D 743 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   LEU D 751 " --> pdb=" O   ASN D 747 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 757 through 767
    Processing helix  chain 'D' and resid 793 through 820
      removed outlier: 3.591A  pdb=" N   TYR D 797 " --> pdb=" O   ALA D 793 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   TYR D 816 " --> pdb=" O   ILE D 812 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 396 through 399
      removed outlier: 6.240A  pdb=" N   VAL A 397 " --> pdb=" O   THR A 443 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 407 through 408
    Processing sheet with id=AA3, first strand: chain 'A' and resid 490 through 491
    Processing sheet with id=AA4, first strand: chain 'A' and resid 702 through 705
      removed outlier: 3.939A  pdb=" N   ILE A 502 " --> pdb=" O   VAL A 723 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 649 through 650
      removed outlier: 5.957A  pdb=" N   THR A 649 " --> pdb=" O   VAL A 683 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 863 through 867
    Processing sheet with id=AA7, first strand: chain 'B' and resid 395 through 397
      removed outlier: 6.899A  pdb=" N   VAL B 395 " --> pdb=" O   LYS B 441 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'B' and resid 407 through 408
    Processing sheet with id=AA9, first strand: chain 'B' and resid 489 through 490
    Processing sheet with id=AB1, first strand: chain 'B' and resid 497 through 498
    Processing sheet with id=AB2, first strand: chain 'B' and resid 702 through 705
      removed outlier: 4.156A  pdb=" N   ILE B 502 " --> pdb=" O   VAL B 723 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 396 through 399
      removed outlier: 6.239A  pdb=" N   VAL C 397 " --> pdb=" O   THR C 443 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'C' and resid 407 through 408
    Processing sheet with id=AB5, first strand: chain 'C' and resid 490 through 491
    Processing sheet with id=AB6, first strand: chain 'C' and resid 702 through 705
      removed outlier: 3.940A  pdb=" N   ILE C 502 " --> pdb=" O   VAL C 723 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 649 through 650
      removed outlier: 5.956A  pdb=" N   THR C 649 " --> pdb=" O   VAL C 683 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB7
    Processing sheet with id=AB8, first strand: chain 'C' and resid 863 through 867
    Processing sheet with id=AB9, first strand: chain 'D' and resid 395 through 397
      removed outlier: 6.899A  pdb=" N   VAL D 395 " --> pdb=" O   LYS D 441 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB9
    Processing sheet with id=AC1, first strand: chain 'D' and resid 407 through 408
    Processing sheet with id=AC2, first strand: chain 'D' and resid 489 through 490
    Processing sheet with id=AC3, first strand: chain 'D' and resid 497 through 498
    Processing sheet with id=AC4, first strand: chain 'D' and resid 702 through 705
      removed outlier: 4.155A  pdb=" N   ILE D 502 " --> pdb=" O   VAL D 723 " (cutoff:3.500A)

    716 hydrogen bonds defined for protein.
    2082 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 4.78

  Time building geometry restraints manager: 4.43 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.22 -     1.35: 4742
        1.35 -     1.47: 4120
        1.47 -     1.59: 6942
        1.59 -     1.71: 0
        1.71 -     1.84: 174
  Bond restraints: 15978
  Sorted by residual:
  bond pdb=" C   THR C 929 "
       pdb=" N   PRO C 930 "
    ideal  model  delta    sigma   weight residual
    1.336  1.394 -0.058 1.25e-02 6.40e+03 2.13e+01
  bond pdb=" C   THR A 929 "
       pdb=" N   PRO A 930 "
    ideal  model  delta    sigma   weight residual
    1.336  1.393 -0.057 1.25e-02 6.40e+03 2.11e+01
  bond pdb=" C   THR B 744 "
       pdb=" N   PRO B 745 "
    ideal  model  delta    sigma   weight residual
    1.336  1.390 -0.055 1.23e-02 6.61e+03 1.99e+01
  bond pdb=" C   THR D 744 "
       pdb=" N   PRO D 745 "
    ideal  model  delta    sigma   weight residual
    1.336  1.390 -0.055 1.23e-02 6.61e+03 1.98e+01
  bond pdb=" C   ASP D 519 "
       pdb=" N   PRO D 520 "
    ideal  model  delta    sigma   weight residual
    1.335  1.380 -0.045 1.30e-02 5.92e+03 1.18e+01
  ... (remaining 15973 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.18: 20203
        2.18 -     4.36: 1064
        4.36 -     6.54: 203
        6.54 -     8.73: 87
        8.73 -    10.91: 13
  Bond angle restraints: 21570
  Sorted by residual:
  angle pdb=" N   LEU C 862 "
        pdb=" CA  LEU C 862 "
        pdb=" C   LEU C 862 "
      ideal   model   delta    sigma   weight residual
     110.42  118.07   -7.65 1.46e+00 4.69e-01 2.74e+01
  angle pdb=" N   LEU A 862 "
        pdb=" CA  LEU A 862 "
        pdb=" C   LEU A 862 "
      ideal   model   delta    sigma   weight residual
     110.42  118.03   -7.61 1.46e+00 4.69e-01 2.71e+01
  angle pdb=" C   GLU D 416 "
        pdb=" N   GLY D 417 "
        pdb=" CA  GLY D 417 "
      ideal   model   delta    sigma   weight residual
     119.99  125.64   -5.65 1.13e+00 7.83e-01 2.50e+01
  angle pdb=" C   GLY C 894 "
        pdb=" N   GLU C 895 "
        pdb=" CA  GLU C 895 "
      ideal   model   delta    sigma   weight residual
     121.54  131.06   -9.52 1.91e+00 2.74e-01 2.48e+01
  angle pdb=" C   GLU B 416 "
        pdb=" N   GLY B 417 "
        pdb=" CA  GLY B 417 "
      ideal   model   delta    sigma   weight residual
     119.99  125.61   -5.62 1.13e+00 7.83e-01 2.47e+01
  ... (remaining 21565 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.25: 8662
       14.25 -    28.51: 543
       28.51 -    42.76: 193
       42.76 -    57.02: 21
       57.02 -    71.27: 12
  Dihedral angle restraints: 9431
    sinusoidal: 3701
      harmonic: 5730
  Sorted by residual:
  dihedral pdb=" CA  LYS C 716 "
           pdb=" C   LYS C 716 "
           pdb=" N   PRO C 717 "
           pdb=" CA  PRO C 717 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -119.81  -60.19     0      5.00e+00 4.00e-02 1.45e+02
  dihedral pdb=" CA  LYS A 716 "
           pdb=" C   LYS A 716 "
           pdb=" N   PRO A 717 "
           pdb=" CA  PRO A 717 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -119.83  -60.17     0      5.00e+00 4.00e-02 1.45e+02
  dihedral pdb=" CA  GLU B 678 "
           pdb=" C   GLU B 678 "
           pdb=" N   PRO B 679 "
           pdb=" CA  PRO B 679 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  133.79   46.21     0      5.00e+00 4.00e-02 8.54e+01
  ... (remaining 9428 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 1751
       0.057 -    0.113: 551
       0.113 -    0.170: 104
       0.170 -    0.226: 20
       0.226 -    0.283: 2
  Chirality restraints: 2428
  Sorted by residual:
  chirality pdb=" CB  ILE B 591 "
            pdb=" CA  ILE B 591 "
            pdb=" CG1 ILE B 591 "
            pdb=" CG2 ILE B 591 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.93   -0.28 2.00e-01 2.50e+01 2.00e+00
  chirality pdb=" CB  ILE D 591 "
            pdb=" CA  ILE D 591 "
            pdb=" CG1 ILE D 591 "
            pdb=" CG2 ILE D 591 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.92   -0.28 2.00e-01 2.50e+01 1.94e+00
  chirality pdb=" CA  PRO B 494 "
            pdb=" N   PRO B 494 "
            pdb=" C   PRO B 494 "
            pdb=" CB  PRO B 494 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.49    0.22 2.00e-01 2.50e+01 1.26e+00
  ... (remaining 2425 not shown)

  Planarity restraints: 2654
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU D 678 "   -0.079 5.00e-02 4.00e+02   1.21e-01 2.33e+01
        pdb=" N   PRO D 679 "    0.209 5.00e-02 4.00e+02
        pdb=" CA  PRO D 679 "   -0.061 5.00e-02 4.00e+02
        pdb=" CD  PRO D 679 "   -0.069 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B 678 "   -0.079 5.00e-02 4.00e+02   1.20e-01 2.32e+01
        pdb=" N   PRO B 679 "    0.208 5.00e-02 4.00e+02
        pdb=" CA  PRO B 679 "   -0.061 5.00e-02 4.00e+02
        pdb=" CD  PRO B 679 "   -0.069 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL C 878 "    0.018 2.00e-02 2.50e+03   3.59e-02 1.29e+01
        pdb=" C   VAL C 878 "   -0.062 2.00e-02 2.50e+03
        pdb=" O   VAL C 878 "    0.023 2.00e-02 2.50e+03
        pdb=" N   LYS C 879 "    0.021 2.00e-02 2.50e+03
  ... (remaining 2651 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 113
        2.60 -     3.18: 12785
        3.18 -     3.75: 23100
        3.75 -     4.33: 32085
        4.33 -     4.90: 52913
  Nonbonded interactions: 120996
  Sorted by model distance:
  nonbonded pdb=" SG  CYS D 718 "
            pdb=" SG  CYS D 773 "
     model   vdw
     2.029 3.760
  nonbonded pdb=" SG  CYS C 718 "
            pdb=" SG  CYS C 773 "
     model   vdw
     2.032 3.760
  nonbonded pdb=" SG  CYS C 890 "
            pdb=" SG  CYS C 900 "
     model   vdw
     2.035 3.760
  nonbonded pdb=" O   ILE C 925 "
            pdb=" OG1 THR C 929 "
     model   vdw
     2.218 3.040
  nonbonded pdb=" O   ILE A 925 "
            pdb=" OG1 THR A 929 "
     model   vdw
     2.219 3.040
  ... (remaining 120991 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 392 through 1035)
  selection = chain 'C'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.130
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.630
  Check model and map are aligned:         0.120
  Set scattering table:                    0.160
  Process input model:                     40.150
  Find NCS groups from input model:        0.550
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   46.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7142
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.066  15978  Z= 0.363
  Angle     :  1.224  10.908  21570  Z= 0.729
  Chirality :  0.057   0.283   2428
  Planarity :  0.008   0.121   2654
  Dihedral  : 11.205  71.275   5766
  Min Nonbonded Distance : 2.029

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  1.12 %
    Allowed  : 10.63 %
    Favored  : 88.25 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  6.58 %
    Favored  : 93.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 10.00 %
    Twisted General : 0.42 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.78 (0.13), residues: 1966
  helix: -3.64 (0.10), residues: 1010
  sheet: -3.71 (0.29), residues: 198
  loop : -3.92 (0.17), residues: 758

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.003   TRP A 861 
 HIS   0.005   0.001   HIS C 412 
 PHE   0.049   0.003   PHE C 891 
 TYR   0.021   0.003   TYR C 533 
 ARG   0.014   0.001   ARG C 897 

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3932 Ramachandran restraints generated.
    1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3932 Ramachandran restraints generated.
    1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  396 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 392
  time to evaluate  : 1.814 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  527 MET cc_start: 0.7378 (ptm) cc_final: 0.5895 (mmt)
REVERT: A  669 LYS cc_start: 0.8209 (mtpm) cc_final: 0.7398 (tmtt)
REVERT: A  888 ARG cc_start: 0.6140 (mmp80) cc_final: 0.5806 (ttm-80)
REVERT: A 1001 TYR cc_start: 0.5863 (p90) cc_final: 0.5556 (p90)
REVERT: B  438 PHE cc_start: 0.8323 (p90) cc_final: 0.8008 (p90)
REVERT: B  695 LYS cc_start: 0.7623 (mtmp) cc_final: 0.7256 (mmpt)
REVERT: B  803 LEU cc_start: 0.8074 (mt) cc_final: 0.7812 (mp)
REVERT: C  500 ILE cc_start: 0.8878 (mt) cc_final: 0.8654 (mt)
REVERT: C  527 MET cc_start: 0.6397 (ptm) cc_final: 0.4304 (mmt)
REVERT: C  619 ASN cc_start: 0.8508 (t0) cc_final: 0.8253 (t0)
REVERT: C  814 PHE cc_start: 0.7335 (t80) cc_final: 0.7061 (t80)
REVERT: D  527 MET cc_start: 0.6718 (mtp) cc_final: 0.6501 (mmt)
  outliers start: 4
  outliers final: 2
  residues processed: 394
  average time/residue: 0.3123
  time to fit residues: 174.8352
Evaluate side-chains
  246 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 244
  time to evaluate  : 1.792 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  399 THR
Chi-restraints excluded: chain C residue  399 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 167 optimal weight:    1.9990
   chunk 150 optimal weight:    0.0670
   chunk 83 optimal weight:    2.9990
   chunk 51 optimal weight:    5.9990
   chunk 101 optimal weight:    4.9990
   chunk 80 optimal weight:    0.0970
   chunk 155 optimal weight:   10.0000
   chunk 60 optimal weight:    0.4980
   chunk 94 optimal weight:    3.9990
   chunk 115 optimal weight:    2.9990
   chunk 179 optimal weight:    0.9980
   overall best weight:    0.7318

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 950 HIS
A1000 ASN
B 575 ASN
B 764 ASN
C 435 HIS
C 747 ASN
C 950 HIS
C 990 ASN
C1000 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7263
moved from start:          0.2925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  15978  Z= 0.219
  Angle     :  0.720   8.706  21570  Z= 0.380
  Chirality :  0.043   0.187   2428
  Planarity :  0.006   0.087   2654
  Dihedral  :  6.451  47.492   2154
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.56 %
    Allowed  :  9.92 %
    Favored  : 89.52 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 11.51 %
    Favored  : 86.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.67 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.55 (0.16), residues: 1966
  helix: -1.39 (0.14), residues: 1048
  sheet: -3.49 (0.34), residues: 176
  loop : -3.40 (0.19), residues: 742

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 766 
 HIS   0.003   0.001   HIS C 883 
 PHE   0.022   0.002   PHE A1028 
 TYR   0.024   0.002   TYR A 980 
 ARG   0.005   0.001   ARG B 594 

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3932 Ramachandran restraints generated.
    1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3932 Ramachandran restraints generated.
    1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 259
  time to evaluate  : 1.686 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  443 THR cc_start: 0.8783 (p) cc_final: 0.8306 (t)
REVERT: A  527 MET cc_start: 0.7130 (ptm) cc_final: 0.5370 (mmt)
REVERT: A  669 LYS cc_start: 0.8538 (mtpm) cc_final: 0.7607 (tmtt)
REVERT: A  695 LYS cc_start: 0.7895 (pptt) cc_final: 0.7210 (ptpt)
REVERT: A  888 ARG cc_start: 0.6185 (mmp80) cc_final: 0.5800 (ttm-80)
REVERT: A  975 VAL cc_start: 0.8661 (m) cc_final: 0.8303 (t)
REVERT: A 1028 PHE cc_start: 0.5611 (t80) cc_final: 0.5330 (t80)
REVERT: A 1029 MET cc_start: 0.6723 (OUTLIER) cc_final: 0.5286 (tmm)
REVERT: B  427 ASP cc_start: 0.8746 (m-30) cc_final: 0.8515 (m-30)
REVERT: C  527 MET cc_start: 0.6299 (ptm) cc_final: 0.4180 (mmt)
REVERT: C  684 ARG cc_start: 0.7136 (mtm110) cc_final: 0.6819 (mpp80)
REVERT: C  807 MET cc_start: 0.5151 (mtp) cc_final: 0.4850 (mtp)
REVERT: C 1028 PHE cc_start: 0.6035 (t80) cc_final: 0.5576 (t80)
REVERT: D  427 ASP cc_start: 0.7894 (m-30) cc_final: 0.7673 (m-30)
REVERT: D  606 TRP cc_start: 0.6171 (m-10) cc_final: 0.5890 (m-10)
REVERT: D  699 LYS cc_start: 0.6876 (mmtt) cc_final: 0.6651 (mmtt)
  outliers start: 40
  outliers final: 16
  residues processed: 288
  average time/residue: 0.2576
  time to fit residues: 112.9244
Evaluate side-chains
  239 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 222
  time to evaluate  : 1.756 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  411 ASN
Chi-restraints excluded: chain A residue  447 ASP
Chi-restraints excluded: chain A residue  519 ASP
Chi-restraints excluded: chain A residue  533 TYR
Chi-restraints excluded: chain A residue  744 THR
Chi-restraints excluded: chain A residue 1029 MET
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  456 ASP
Chi-restraints excluded: chain C residue  399 THR
Chi-restraints excluded: chain C residue  412 HIS
Chi-restraints excluded: chain C residue  447 ASP
Chi-restraints excluded: chain C residue  533 TYR
Chi-restraints excluded: chain C residue  630 VAL
Chi-restraints excluded: chain C residue  742 LEU
Chi-restraints excluded: chain D residue  406 VAL
Chi-restraints excluded: chain D residue  456 ASP
Chi-restraints excluded: chain D residue  482 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 99 optimal weight:    2.9990
   chunk 55 optimal weight:   20.0000
   chunk 149 optimal weight:   10.0000
   chunk 122 optimal weight:    8.9990
   chunk 49 optimal weight:   10.0000
   chunk 180 optimal weight:    0.0170
   chunk 194 optimal weight:    4.9990
   chunk 160 optimal weight:    7.9990
   chunk 178 optimal weight:    0.5980
   chunk 61 optimal weight:    9.9990
   chunk 144 optimal weight:    8.9990
   overall best weight:    3.3224

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 747 ASN
A 990 ASN
C 508 GLN
C 726 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7526
moved from start:          0.4269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.086  15978  Z= 0.571
  Angle     :  0.864  10.244  21570  Z= 0.451
  Chirality :  0.052   0.244   2428
  Planarity :  0.007   0.100   2654
  Dihedral  :  6.652  50.484   2153
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 11.65
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  : 12.46 %
    Favored  : 87.08 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 12.87 %
    Favored  : 83.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.67 %
    Twisted General : 0.21 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.96 (0.17), residues: 1966
  helix: -0.75 (0.15), residues: 1040
  sheet: -3.63 (0.33), residues: 182
  loop : -3.23 (0.20), residues: 744

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP D 606 
 HIS   0.006   0.001   HIS D 435 
 PHE   0.030   0.003   PHE D 623 
 TYR   0.038   0.003   TYR A 533 
 ARG   0.004   0.001   ARG B 453 

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3932 Ramachandran restraints generated.
    1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3932 Ramachandran restraints generated.
    1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  282 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 229
  time to evaluate  : 1.847 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  420 ARG cc_start: 0.7714 (mtm180) cc_final: 0.7346 (mtp85)
REVERT: A  440 TYR cc_start: 0.8516 (OUTLIER) cc_final: 0.7798 (p90)
REVERT: A  518 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8450 (pp)
REVERT: A  527 MET cc_start: 0.7205 (ptm) cc_final: 0.5915 (mmt)
REVERT: A  669 LYS cc_start: 0.8397 (mtpm) cc_final: 0.7592 (tmtt)
REVERT: A  674 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8220 (mtp)
REVERT: A  888 ARG cc_start: 0.6418 (mmp80) cc_final: 0.5776 (ttm-80)
REVERT: A  967 ILE cc_start: 0.7893 (mp) cc_final: 0.7685 (pt)
REVERT: A  975 VAL cc_start: 0.8688 (m) cc_final: 0.8348 (p)
REVERT: A 1001 TYR cc_start: 0.6000 (p90) cc_final: 0.5624 (p90)
REVERT: B  601 VAL cc_start: 0.8476 (t) cc_final: 0.8131 (m)
REVERT: B  639 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8127 (tt)
REVERT: B  688 GLU cc_start: 0.7889 (mp0) cc_final: 0.7676 (mp0)
REVERT: C  408 MET cc_start: 0.8044 (mmt) cc_final: 0.7781 (mmm)
REVERT: C  440 TYR cc_start: 0.8395 (p90) cc_final: 0.8083 (p90)
REVERT: C  518 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8287 (pp)
REVERT: C  527 MET cc_start: 0.6448 (ptm) cc_final: 0.4842 (mmt)
REVERT: C  634 GLU cc_start: 0.8512 (tm-30) cc_final: 0.7855 (tm-30)
REVERT: C  638 ASP cc_start: 0.8275 (m-30) cc_final: 0.8065 (m-30)
REVERT: C  669 LYS cc_start: 0.8153 (mtpm) cc_final: 0.7153 (tmtt)
REVERT: C  684 ARG cc_start: 0.7483 (mtm110) cc_final: 0.7163 (mpp80)
REVERT: C 1029 MET cc_start: 0.6086 (mmm) cc_final: 0.5506 (mmm)
REVERT: D  633 ILE cc_start: 0.8117 (OUTLIER) cc_final: 0.7903 (pp)
REVERT: D  639 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8496 (tt)
  outliers start: 53
  outliers final: 25
  residues processed: 268
  average time/residue: 0.2934
  time to fit residues: 119.0989
Evaluate side-chains
  237 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 205
  time to evaluate  : 1.765 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  411 ASN
Chi-restraints excluded: chain A residue  440 TYR
Chi-restraints excluded: chain A residue  447 ASP
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  518 LEU
Chi-restraints excluded: chain A residue  519 ASP
Chi-restraints excluded: chain A residue  533 TYR
Chi-restraints excluded: chain A residue  649 THR
Chi-restraints excluded: chain A residue  674 MET
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  456 ASP
Chi-restraints excluded: chain B residue  633 ILE
Chi-restraints excluded: chain B residue  639 LEU
Chi-restraints excluded: chain B residue  741 SER
Chi-restraints excluded: chain B residue  785 SER
Chi-restraints excluded: chain B residue  790 SER
Chi-restraints excluded: chain C residue  399 THR
Chi-restraints excluded: chain C residue  447 ASP
Chi-restraints excluded: chain C residue  459 ILE
Chi-restraints excluded: chain C residue  518 LEU
Chi-restraints excluded: chain C residue  519 ASP
Chi-restraints excluded: chain C residue  533 TYR
Chi-restraints excluded: chain C residue  630 VAL
Chi-restraints excluded: chain C residue  645 ILE
Chi-restraints excluded: chain C residue  683 VAL
Chi-restraints excluded: chain C residue  742 LEU
Chi-restraints excluded: chain D residue  445 VAL
Chi-restraints excluded: chain D residue  456 ASP
Chi-restraints excluded: chain D residue  543 VAL
Chi-restraints excluded: chain D residue  633 ILE
Chi-restraints excluded: chain D residue  639 LEU
Chi-restraints excluded: chain D residue  790 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 177 optimal weight:    0.7980
   chunk 135 optimal weight:    4.9990
   chunk 93 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 85 optimal weight:    3.9990
   chunk 120 optimal weight:    0.9980
   chunk 180 optimal weight:    0.9990
   chunk 191 optimal weight:    0.9980
   chunk 94 optimal weight:    1.9990
   chunk 171 optimal weight:    0.8980
   chunk 51 optimal weight:   20.0000
   overall best weight:    0.8980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 642 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7397
moved from start:          0.4499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  15978  Z= 0.217
  Angle     :  0.648  10.496  21570  Z= 0.340
  Chirality :  0.042   0.150   2428
  Planarity :  0.005   0.083   2654
  Dihedral  :  6.013  46.108   2153
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 10.17 %
    Favored  : 89.62 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 14.83 %
    Favored  : 82.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.67 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.16 (0.18), residues: 1966
  helix:  0.03 (0.16), residues: 1046
  sheet: -3.43 (0.35), residues: 154
  loop : -3.10 (0.20), residues: 766

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 766 
 HIS   0.005   0.001   HIS A 412 
 PHE   0.023   0.002   PHE D 623 
 TYR   0.019   0.001   TYR A 980 
 ARG   0.005   0.000   ARG D 594 

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3932 Ramachandran restraints generated.
    1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3932 Ramachandran restraints generated.
    1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  283 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 233
  time to evaluate  : 1.683 
Fit side-chains
   revert: symmetry clash
REVERT: A  420 ARG cc_start: 0.7542 (mtm180) cc_final: 0.7218 (mtp85)
REVERT: A  527 MET cc_start: 0.7148 (ptm) cc_final: 0.5495 (mmt)
REVERT: A  585 MET cc_start: 0.6476 (mmt) cc_final: 0.6250 (mmt)
REVERT: A  663 LYS cc_start: 0.8156 (mmtm) cc_final: 0.7912 (mmtp)
REVERT: A  669 LYS cc_start: 0.8286 (mtpm) cc_final: 0.7548 (tmtt)
REVERT: A  670 MET cc_start: 0.8599 (mtt) cc_final: 0.8268 (mtp)
REVERT: A  674 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.8030 (mtp)
REVERT: A  888 ARG cc_start: 0.6360 (mmp80) cc_final: 0.5652 (ttm-80)
REVERT: A  936 LEU cc_start: 0.6421 (OUTLIER) cc_final: 0.6052 (mt)
REVERT: A  975 VAL cc_start: 0.8712 (m) cc_final: 0.8353 (p)
REVERT: A  981 ILE cc_start: 0.7096 (mt) cc_final: 0.6775 (mm)
REVERT: A 1001 TYR cc_start: 0.5860 (p90) cc_final: 0.5534 (p90)
REVERT: A 1028 PHE cc_start: 0.5618 (t80) cc_final: 0.5343 (t80)
REVERT: B  527 MET cc_start: 0.7663 (mtp) cc_final: 0.6943 (mmt)
REVERT: B  601 VAL cc_start: 0.8291 (t) cc_final: 0.7990 (m)
REVERT: C  518 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8294 (pp)
REVERT: C  527 MET cc_start: 0.6264 (ptm) cc_final: 0.4745 (mmt)
REVERT: C  634 GLU cc_start: 0.8520 (tm-30) cc_final: 0.7825 (tm-30)
REVERT: C  638 ASP cc_start: 0.8165 (m-30) cc_final: 0.7930 (m-30)
REVERT: C  669 LYS cc_start: 0.8186 (mtpm) cc_final: 0.7207 (tmtt)
REVERT: C  880 MET cc_start: 0.3179 (mmp) cc_final: 0.2961 (mmt)
REVERT: C 1028 PHE cc_start: 0.6192 (t80) cc_final: 0.5919 (t80)
REVERT: D  650 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7410 (tt)
  outliers start: 50
  outliers final: 23
  residues processed: 267
  average time/residue: 0.2659
  time to fit residues: 107.5830
Evaluate side-chains
  239 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 212
  time to evaluate  : 1.664 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  411 ASN
Chi-restraints excluded: chain A residue  447 ASP
Chi-restraints excluded: chain A residue  533 TYR
Chi-restraints excluded: chain A residue  649 THR
Chi-restraints excluded: chain A residue  674 MET
Chi-restraints excluded: chain A residue  704 LEU
Chi-restraints excluded: chain A residue  936 LEU
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  456 ASP
Chi-restraints excluded: chain B residue  633 ILE
Chi-restraints excluded: chain B residue  785 SER
Chi-restraints excluded: chain C residue  399 THR
Chi-restraints excluded: chain C residue  407 MET
Chi-restraints excluded: chain C residue  447 ASP
Chi-restraints excluded: chain C residue  518 LEU
Chi-restraints excluded: chain C residue  525 ILE
Chi-restraints excluded: chain C residue  533 TYR
Chi-restraints excluded: chain C residue  630 VAL
Chi-restraints excluded: chain C residue  645 ILE
Chi-restraints excluded: chain C residue  742 LEU
Chi-restraints excluded: chain C residue  900 CYS
Chi-restraints excluded: chain D residue  445 VAL
Chi-restraints excluded: chain D residue  456 ASP
Chi-restraints excluded: chain D residue  482 THR
Chi-restraints excluded: chain D residue  543 VAL
Chi-restraints excluded: chain D residue  650 LEU
Chi-restraints excluded: chain D residue  741 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 159 optimal weight:    1.9990
   chunk 108 optimal weight:    0.0170
   chunk 2 optimal weight:    0.0670
   chunk 142 optimal weight:   20.0000
   chunk 78 optimal weight:    0.8980
   chunk 163 optimal weight:    1.9990
   chunk 132 optimal weight:    0.5980
   chunk 0 optimal weight:    2.9990
   chunk 97 optimal weight:    0.7980
   chunk 171 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   overall best weight:    0.4756

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 619 ASN
C 435 HIS
C 642 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7332
moved from start:          0.4789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  15978  Z= 0.168
  Angle     :  0.616  14.726  21570  Z= 0.317
  Chirality :  0.041   0.185   2428
  Planarity :  0.005   0.072   2654
  Dihedral  :  5.590  41.450   2153
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  : 10.07 %
    Favored  : 89.78 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 15.30 %
    Favored  : 82.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.67 %
    Twisted General : 0.05 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.66 (0.19), residues: 1966
  helix:  0.52 (0.16), residues: 1044
  sheet: -3.41 (0.35), residues: 152
  loop : -2.95 (0.20), residues: 770

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.001   TRP D 606 
 HIS   0.001   0.001   HIS C 412 
 PHE   0.023   0.001   PHE D 623 
 TYR   0.021   0.001   TYR A 980 
 ARG   0.004   0.000   ARG D 594 

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3932 Ramachandran restraints generated.
    1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3932 Ramachandran restraints generated.
    1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  272 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 227
  time to evaluate  : 1.739 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  408 MET cc_start: 0.8045 (mmm) cc_final: 0.7535 (mmm)
REVERT: A  420 ARG cc_start: 0.7537 (mtm180) cc_final: 0.7174 (mtp85)
REVERT: A  440 TYR cc_start: 0.8227 (OUTLIER) cc_final: 0.7528 (p90)
REVERT: A  527 MET cc_start: 0.7074 (ptm) cc_final: 0.5395 (mmt)
REVERT: A  669 LYS cc_start: 0.8263 (mtpm) cc_final: 0.7459 (tmtt)
REVERT: A  670 MET cc_start: 0.8426 (mtt) cc_final: 0.8217 (mtp)
REVERT: A  674 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.8139 (mtp)
REVERT: A  888 ARG cc_start: 0.6226 (mmp80) cc_final: 0.5533 (ttm-80)
REVERT: A  907 MET cc_start: 0.6888 (ptp) cc_final: 0.6687 (ptp)
REVERT: A  936 LEU cc_start: 0.6548 (OUTLIER) cc_final: 0.6200 (mt)
REVERT: A 1001 TYR cc_start: 0.5741 (p90) cc_final: 0.5410 (p90)
REVERT: A 1028 PHE cc_start: 0.5455 (t80) cc_final: 0.5236 (t80)
REVERT: B  527 MET cc_start: 0.7458 (mtp) cc_final: 0.6791 (mmt)
REVERT: B  591 ILE cc_start: 0.3619 (OUTLIER) cc_final: 0.3056 (pt)
REVERT: C  466 GLU cc_start: 0.7077 (mt-10) cc_final: 0.6841 (tt0)
REVERT: C  527 MET cc_start: 0.6312 (ptm) cc_final: 0.4564 (mmt)
REVERT: C  585 MET cc_start: 0.5813 (mmt) cc_final: 0.5582 (mmt)
REVERT: C  634 GLU cc_start: 0.8494 (tm-30) cc_final: 0.7875 (tm-30)
REVERT: C  669 LYS cc_start: 0.8294 (mtpm) cc_final: 0.7240 (tmtt)
REVERT: C  674 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7848 (mtp)
REVERT: C 1028 PHE cc_start: 0.6409 (t80) cc_final: 0.6107 (t80)
REVERT: D  531 PHE cc_start: 0.5720 (m-10) cc_final: 0.5496 (m-10)
REVERT: D  633 ILE cc_start: 0.8082 (OUTLIER) cc_final: 0.7845 (pp)
REVERT: D  650 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.7242 (tt)
REVERT: D  688 GLU cc_start: 0.7703 (mp0) cc_final: 0.7486 (mp0)
  outliers start: 45
  outliers final: 22
  residues processed: 254
  average time/residue: 0.2605
  time to fit residues: 100.9875
Evaluate side-chains
  233 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 204
  time to evaluate  : 1.821 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  411 ASN
Chi-restraints excluded: chain A residue  440 TYR
Chi-restraints excluded: chain A residue  447 ASP
Chi-restraints excluded: chain A residue  533 TYR
Chi-restraints excluded: chain A residue  538 VAL
Chi-restraints excluded: chain A residue  630 VAL
Chi-restraints excluded: chain A residue  649 THR
Chi-restraints excluded: chain A residue  674 MET
Chi-restraints excluded: chain A residue  734 ILE
Chi-restraints excluded: chain A residue  936 LEU
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  456 ASP
Chi-restraints excluded: chain B residue  591 ILE
Chi-restraints excluded: chain B residue  633 ILE
Chi-restraints excluded: chain B residue  741 SER
Chi-restraints excluded: chain B residue  790 SER
Chi-restraints excluded: chain C residue  399 THR
Chi-restraints excluded: chain C residue  406 VAL
Chi-restraints excluded: chain C residue  447 ASP
Chi-restraints excluded: chain C residue  533 TYR
Chi-restraints excluded: chain C residue  630 VAL
Chi-restraints excluded: chain C residue  674 MET
Chi-restraints excluded: chain C residue  742 LEU
Chi-restraints excluded: chain C residue  900 CYS
Chi-restraints excluded: chain D residue  445 VAL
Chi-restraints excluded: chain D residue  456 ASP
Chi-restraints excluded: chain D residue  482 THR
Chi-restraints excluded: chain D residue  633 ILE
Chi-restraints excluded: chain D residue  650 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 64 optimal weight:    1.9990
   chunk 172 optimal weight:   10.0000
   chunk 37 optimal weight:    0.9980
   chunk 112 optimal weight:    0.6980
   chunk 47 optimal weight:    6.9990
   chunk 191 optimal weight:    1.9990
   chunk 159 optimal weight:    0.0770
   chunk 88 optimal weight:    2.9990
   chunk 15 optimal weight:    9.9990
   chunk 63 optimal weight:    2.9990
   chunk 100 optimal weight:    0.5980
   overall best weight:    0.8740

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
C 642 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7366
moved from start:          0.4976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  15978  Z= 0.211
  Angle     :  0.628  14.917  21570  Z= 0.324
  Chirality :  0.042   0.188   2428
  Planarity :  0.005   0.088   2654
  Dihedral  :  5.497  41.297   2153
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 9.93
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 10.63 %
    Favored  : 89.17 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 16.31 %
    Favored  : 81.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.67 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.48 (0.19), residues: 1966
  helix:  0.65 (0.16), residues: 1052
  sheet: -3.31 (0.35), residues: 152
  loop : -2.89 (0.21), residues: 762

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.048   0.001   TRP D 606 
 HIS   0.002   0.001   HIS B 435 
 PHE   0.021   0.001   PHE D 623 
 TYR   0.019   0.001   TYR A 980 
 ARG   0.003   0.000   ARG D 594 

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3932 Ramachandran restraints generated.
    1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3932 Ramachandran restraints generated.
    1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 215
  time to evaluate  : 1.970 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  408 MET cc_start: 0.7958 (mmm) cc_final: 0.7370 (mmm)
REVERT: A  414 MET cc_start: 0.6979 (ptp) cc_final: 0.6572 (ptp)
REVERT: A  420 ARG cc_start: 0.7530 (mtm180) cc_final: 0.7090 (mtp85)
REVERT: A  527 MET cc_start: 0.7132 (ptm) cc_final: 0.5447 (mmt)
REVERT: A  669 LYS cc_start: 0.8271 (mtpm) cc_final: 0.7449 (tmtt)
REVERT: A  674 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8212 (mtp)
REVERT: A  734 ILE cc_start: 0.8268 (OUTLIER) cc_final: 0.8057 (mm)
REVERT: A  888 ARG cc_start: 0.6128 (mmp80) cc_final: 0.5693 (ttm-80)
REVERT: A  907 MET cc_start: 0.6893 (ptp) cc_final: 0.6667 (ptp)
REVERT: A  936 LEU cc_start: 0.6500 (OUTLIER) cc_final: 0.6172 (mt)
REVERT: A 1001 TYR cc_start: 0.5771 (p90) cc_final: 0.5454 (p90)
REVERT: A 1028 PHE cc_start: 0.5547 (t80) cc_final: 0.5331 (t80)
REVERT: B  527 MET cc_start: 0.7461 (mtp) cc_final: 0.6883 (mmt)
REVERT: B  591 ILE cc_start: 0.3424 (OUTLIER) cc_final: 0.2916 (pt)
REVERT: B  688 GLU cc_start: 0.7827 (mp0) cc_final: 0.7575 (mp0)
REVERT: C  527 MET cc_start: 0.6346 (ptm) cc_final: 0.4641 (mmt)
REVERT: C  634 GLU cc_start: 0.8461 (tm-30) cc_final: 0.7794 (tm-30)
REVERT: C  669 LYS cc_start: 0.8309 (mtpm) cc_final: 0.7450 (tmtt)
REVERT: C  674 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.7870 (mtp)
REVERT: C  880 MET cc_start: 0.4679 (mpp) cc_final: 0.3802 (mmp)
REVERT: C  988 MET cc_start: 0.7546 (tmm) cc_final: 0.7298 (tmm)
REVERT: C 1028 PHE cc_start: 0.6458 (t80) cc_final: 0.6147 (t80)
REVERT: D  531 PHE cc_start: 0.5762 (m-10) cc_final: 0.5477 (m-10)
REVERT: D  606 TRP cc_start: 0.6830 (m-90) cc_final: 0.6436 (m-90)
REVERT: D  633 ILE cc_start: 0.8082 (OUTLIER) cc_final: 0.7840 (pp)
REVERT: D  688 GLU cc_start: 0.7631 (mp0) cc_final: 0.7387 (mp0)
  outliers start: 43
  outliers final: 25
  residues processed: 242
  average time/residue: 0.2646
  time to fit residues: 98.0022
Evaluate side-chains
  237 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 206
  time to evaluate  : 1.863 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  411 ASN
Chi-restraints excluded: chain A residue  447 ASP
Chi-restraints excluded: chain A residue  533 TYR
Chi-restraints excluded: chain A residue  630 VAL
Chi-restraints excluded: chain A residue  649 THR
Chi-restraints excluded: chain A residue  674 MET
Chi-restraints excluded: chain A residue  734 ILE
Chi-restraints excluded: chain A residue  868 ILE
Chi-restraints excluded: chain A residue  936 LEU
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  456 ASP
Chi-restraints excluded: chain B residue  591 ILE
Chi-restraints excluded: chain B residue  633 ILE
Chi-restraints excluded: chain B residue  741 SER
Chi-restraints excluded: chain B residue  785 SER
Chi-restraints excluded: chain B residue  790 SER
Chi-restraints excluded: chain C residue  406 VAL
Chi-restraints excluded: chain C residue  447 ASP
Chi-restraints excluded: chain C residue  533 TYR
Chi-restraints excluded: chain C residue  630 VAL
Chi-restraints excluded: chain C residue  674 MET
Chi-restraints excluded: chain C residue  734 ILE
Chi-restraints excluded: chain C residue  742 LEU
Chi-restraints excluded: chain C residue  900 CYS
Chi-restraints excluded: chain D residue  445 VAL
Chi-restraints excluded: chain D residue  456 ASP
Chi-restraints excluded: chain D residue  482 THR
Chi-restraints excluded: chain D residue  543 VAL
Chi-restraints excluded: chain D residue  633 ILE
Chi-restraints excluded: chain D residue  741 SER
Chi-restraints excluded: chain D residue  790 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 184 optimal weight:    4.9990
   chunk 21 optimal weight:    0.0060
   chunk 109 optimal weight:    0.5980
   chunk 139 optimal weight:   30.0000
   chunk 108 optimal weight:    0.6980
   chunk 161 optimal weight:    0.7980
   chunk 106 optimal weight:    0.5980
   chunk 190 optimal weight:    0.0170
   chunk 119 optimal weight:    0.5980
   chunk 116 optimal weight:    3.9990
   chunk 88 optimal weight:    2.9990
   overall best weight:    0.3634

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 619 ASN
C 642 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7296
moved from start:          0.5174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045  15978  Z= 0.161
  Angle     :  0.603  14.767  21570  Z= 0.310
  Chirality :  0.041   0.154   2428
  Planarity :  0.005   0.078   2654
  Dihedral  :  5.291  39.471   2152
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  9.82 %
    Favored  : 90.03 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 17.97 %
    Favored  : 80.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.67 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.24 (0.19), residues: 1966
  helix:  0.88 (0.16), residues: 1054
  sheet: -3.01 (0.35), residues: 176
  loop : -2.86 (0.21), residues: 736

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.001   TRP D 606 
 HIS   0.001   0.000   HIS C 412 
 PHE   0.024   0.001   PHE D 623 
 TYR   0.022   0.001   TYR C 702 
 ARG   0.003   0.000   ARG D 594 

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3932 Ramachandran restraints generated.
    1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3932 Ramachandran restraints generated.
    1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 232
  time to evaluate  : 1.789 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  408 MET cc_start: 0.7943 (mmm) cc_final: 0.7327 (mmm)
REVERT: A  414 MET cc_start: 0.6965 (ptp) cc_final: 0.6594 (ptp)
REVERT: A  420 ARG cc_start: 0.7433 (mtm180) cc_final: 0.7009 (mtp85)
REVERT: A  527 MET cc_start: 0.6979 (ptm) cc_final: 0.5261 (mmt)
REVERT: A  585 MET cc_start: 0.4857 (mmt) cc_final: 0.4547 (mmt)
REVERT: A  599 ARG cc_start: 0.7085 (mtt90) cc_final: 0.6723 (mmt90)
REVERT: A  669 LYS cc_start: 0.8262 (mtpm) cc_final: 0.7463 (tmtt)
REVERT: A  888 ARG cc_start: 0.6098 (mmp80) cc_final: 0.5671 (ttm-80)
REVERT: A  907 MET cc_start: 0.6895 (ptp) cc_final: 0.6658 (ptp)
REVERT: A  936 LEU cc_start: 0.6564 (OUTLIER) cc_final: 0.6305 (mt)
REVERT: A 1001 TYR cc_start: 0.5798 (p90) cc_final: 0.5488 (p90)
REVERT: B  527 MET cc_start: 0.7276 (mtp) cc_final: 0.6808 (mmt)
REVERT: B  688 GLU cc_start: 0.7736 (mp0) cc_final: 0.7459 (mp0)
REVERT: C  398 THR cc_start: 0.8921 (p) cc_final: 0.8128 (m)
REVERT: C  527 MET cc_start: 0.6467 (ptm) cc_final: 0.4640 (mmt)
REVERT: C  627 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7684 (tm-30)
REVERT: C  634 GLU cc_start: 0.8480 (tm-30) cc_final: 0.7825 (tm-30)
REVERT: C  669 LYS cc_start: 0.8429 (mtpm) cc_final: 0.7464 (tmtt)
REVERT: C  714 GLN cc_start: 0.7681 (mm-40) cc_final: 0.7454 (mm110)
REVERT: C  880 MET cc_start: 0.4602 (mpp) cc_final: 0.3931 (ttm)
REVERT: C  988 MET cc_start: 0.7468 (tmm) cc_final: 0.7224 (tmm)
REVERT: C 1028 PHE cc_start: 0.6244 (t80) cc_final: 0.5964 (t80)
REVERT: D  531 PHE cc_start: 0.5833 (m-10) cc_final: 0.5542 (m-10)
REVERT: D  606 TRP cc_start: 0.6619 (m-10) cc_final: 0.6397 (m-90)
REVERT: D  633 ILE cc_start: 0.8051 (OUTLIER) cc_final: 0.7818 (pp)
  outliers start: 34
  outliers final: 20
  residues processed: 251
  average time/residue: 0.2840
  time to fit residues: 107.2051
Evaluate side-chains
  225 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 203
  time to evaluate  : 1.757 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  411 ASN
Chi-restraints excluded: chain A residue  447 ASP
Chi-restraints excluded: chain A residue  533 TYR
Chi-restraints excluded: chain A residue  630 VAL
Chi-restraints excluded: chain A residue  649 THR
Chi-restraints excluded: chain A residue  868 ILE
Chi-restraints excluded: chain A residue  936 LEU
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  456 ASP
Chi-restraints excluded: chain B residue  681 VAL
Chi-restraints excluded: chain B residue  741 SER
Chi-restraints excluded: chain B residue  785 SER
Chi-restraints excluded: chain C residue  407 MET
Chi-restraints excluded: chain C residue  533 TYR
Chi-restraints excluded: chain C residue  630 VAL
Chi-restraints excluded: chain C residue  683 VAL
Chi-restraints excluded: chain C residue  900 CYS
Chi-restraints excluded: chain D residue  445 VAL
Chi-restraints excluded: chain D residue  456 ASP
Chi-restraints excluded: chain D residue  482 THR
Chi-restraints excluded: chain D residue  633 ILE
Chi-restraints excluded: chain D residue  790 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 118 optimal weight:    3.9990
   chunk 76 optimal weight:    8.9990
   chunk 113 optimal weight:    0.8980
   chunk 57 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 36 optimal weight:    4.9990
   chunk 121 optimal weight:    8.9990
   chunk 130 optimal weight:    0.8980
   chunk 94 optimal weight:    0.4980
   chunk 17 optimal weight:    4.9990
   chunk 150 optimal weight:    8.9990
   overall best weight:    1.6584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
C 642 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7427
moved from start:          0.5260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.069  15978  Z= 0.318
  Angle     :  0.682  15.420  21570  Z= 0.350
  Chirality :  0.044   0.240   2428
  Planarity :  0.005   0.094   2654
  Dihedral  :  5.511  40.483   2152
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  : 10.99 %
    Favored  : 88.71 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 18.03 %
    Favored  : 79.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.67 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.42 (0.19), residues: 1966
  helix:  0.66 (0.16), residues: 1060
  sheet: -3.17 (0.37), residues: 150
  loop : -2.86 (0.21), residues: 756

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP D 606 
 HIS   0.003   0.001   HIS B 435 
 PHE   0.028   0.002   PHE B 541 
 TYR   0.024   0.002   TYR A 702 
 ARG   0.012   0.000   ARG D 661 

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3932 Ramachandran restraints generated.
    1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3932 Ramachandran restraints generated.
    1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 211
  time to evaluate  : 1.558 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  408 MET cc_start: 0.8005 (mmm) cc_final: 0.7398 (mmm)
REVERT: A  414 MET cc_start: 0.6969 (ptp) cc_final: 0.6595 (ptp)
REVERT: A  420 ARG cc_start: 0.7634 (mtm180) cc_final: 0.7120 (mtp85)
REVERT: A  527 MET cc_start: 0.7191 (ptm) cc_final: 0.5581 (mmt)
REVERT: A  585 MET cc_start: 0.5983 (mmt) cc_final: 0.5356 (mmt)
REVERT: A  599 ARG cc_start: 0.7225 (mtt90) cc_final: 0.6978 (mmt90)
REVERT: A  663 LYS cc_start: 0.8109 (mmtm) cc_final: 0.7883 (mmtp)
REVERT: A  669 LYS cc_start: 0.8277 (mtpm) cc_final: 0.7457 (tmtt)
REVERT: A  888 ARG cc_start: 0.6142 (mmp80) cc_final: 0.5709 (ttm-80)
REVERT: A  936 LEU cc_start: 0.6268 (OUTLIER) cc_final: 0.6012 (mt)
REVERT: A 1001 TYR cc_start: 0.5898 (p90) cc_final: 0.5611 (p90)
REVERT: B  419 GLU cc_start: 0.8201 (mp0) cc_final: 0.7402 (mp0)
REVERT: B  527 MET cc_start: 0.7598 (mtp) cc_final: 0.7072 (mmt)
REVERT: B  601 VAL cc_start: 0.8045 (t) cc_final: 0.7766 (m)
REVERT: B  688 GLU cc_start: 0.7803 (mp0) cc_final: 0.7499 (mp0)
REVERT: C  527 MET cc_start: 0.6485 (ptm) cc_final: 0.4720 (mmt)
REVERT: C  627 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7658 (tm-30)
REVERT: C  634 GLU cc_start: 0.8515 (tm-30) cc_final: 0.7819 (tm-30)
REVERT: C  669 LYS cc_start: 0.8473 (mtpm) cc_final: 0.7521 (tptp)
REVERT: C  674 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.8178 (mtp)
REVERT: C  714 GLN cc_start: 0.7944 (mm-40) cc_final: 0.7719 (mm110)
REVERT: C  880 MET cc_start: 0.4519 (mpp) cc_final: 0.3791 (mpp)
REVERT: C 1028 PHE cc_start: 0.6121 (t80) cc_final: 0.5781 (t80)
REVERT: D  531 PHE cc_start: 0.6013 (m-10) cc_final: 0.5720 (m-10)
REVERT: D  606 TRP cc_start: 0.6925 (m-10) cc_final: 0.6509 (m-90)
REVERT: D  633 ILE cc_start: 0.8104 (OUTLIER) cc_final: 0.7871 (pp)
  outliers start: 40
  outliers final: 25
  residues processed: 234
  average time/residue: 0.2670
  time to fit residues: 94.6248
Evaluate side-chains
  233 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 205
  time to evaluate  : 1.863 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  411 ASN
Chi-restraints excluded: chain A residue  447 ASP
Chi-restraints excluded: chain A residue  533 TYR
Chi-restraints excluded: chain A residue  542 LEU
Chi-restraints excluded: chain A residue  630 VAL
Chi-restraints excluded: chain A residue  649 THR
Chi-restraints excluded: chain A residue  868 ILE
Chi-restraints excluded: chain A residue  936 LEU
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  456 ASP
Chi-restraints excluded: chain B residue  681 VAL
Chi-restraints excluded: chain B residue  741 SER
Chi-restraints excluded: chain B residue  785 SER
Chi-restraints excluded: chain B residue  790 SER
Chi-restraints excluded: chain C residue  447 ASP
Chi-restraints excluded: chain C residue  533 TYR
Chi-restraints excluded: chain C residue  538 VAL
Chi-restraints excluded: chain C residue  630 VAL
Chi-restraints excluded: chain C residue  674 MET
Chi-restraints excluded: chain C residue  683 VAL
Chi-restraints excluded: chain C residue  900 CYS
Chi-restraints excluded: chain D residue  445 VAL
Chi-restraints excluded: chain D residue  456 ASP
Chi-restraints excluded: chain D residue  482 THR
Chi-restraints excluded: chain D residue  543 VAL
Chi-restraints excluded: chain D residue  633 ILE
Chi-restraints excluded: chain D residue  741 SER
Chi-restraints excluded: chain D residue  790 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 173 optimal weight:    7.9990
   chunk 182 optimal weight:    2.9990
   chunk 166 optimal weight:    0.9990
   chunk 177 optimal weight:    0.5980
   chunk 107 optimal weight:    0.4980
   chunk 77 optimal weight:    5.9990
   chunk 139 optimal weight:   30.0000
   chunk 54 optimal weight:    7.9990
   chunk 160 optimal weight:    9.9990
   chunk 168 optimal weight:    0.8980
   chunk 116 optimal weight:    1.9990
   overall best weight:    0.9984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 954 HIS
C 642 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7380
moved from start:          0.5371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  15978  Z= 0.228
  Angle     :  0.642  15.670  21570  Z= 0.329
  Chirality :  0.042   0.229   2428
  Planarity :  0.005   0.090   2654
  Dihedral  :  5.404  39.392   2152
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 10.07 %
    Favored  : 89.73 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 18.27 %
    Favored  : 79.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.67 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.28 (0.19), residues: 1966
  helix:  0.77 (0.16), residues: 1062
  sheet: -3.12 (0.37), residues: 152
  loop : -2.80 (0.21), residues: 752

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP D 606 
 HIS   0.002   0.001   HIS B 435 
 PHE   0.025   0.001   PHE B 541 
 TYR   0.017   0.001   TYR A 702 
 ARG   0.011   0.000   ARG D 661 

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3932 Ramachandran restraints generated.
    1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3932 Ramachandran restraints generated.
    1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 206
  time to evaluate  : 1.763 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  408 MET cc_start: 0.7993 (mmm) cc_final: 0.7335 (mmm)
REVERT: A  414 MET cc_start: 0.6903 (ptp) cc_final: 0.6499 (ptp)
REVERT: A  527 MET cc_start: 0.7007 (ptm) cc_final: 0.5372 (mmt)
REVERT: A  585 MET cc_start: 0.5989 (mmt) cc_final: 0.5184 (mmt)
REVERT: A  599 ARG cc_start: 0.7214 (mtt90) cc_final: 0.6963 (mmt90)
REVERT: A  669 LYS cc_start: 0.8387 (mtpm) cc_final: 0.7420 (tmtt)
REVERT: A  888 ARG cc_start: 0.6123 (mmp80) cc_final: 0.5712 (ttm-80)
REVERT: A  936 LEU cc_start: 0.6226 (OUTLIER) cc_final: 0.6006 (mt)
REVERT: A 1001 TYR cc_start: 0.5900 (p90) cc_final: 0.5643 (p90)
REVERT: B  419 GLU cc_start: 0.8234 (mp0) cc_final: 0.7450 (mp0)
REVERT: B  527 MET cc_start: 0.7347 (mtp) cc_final: 0.6904 (mmt)
REVERT: C  527 MET cc_start: 0.6372 (ptm) cc_final: 0.4618 (mmt)
REVERT: C  627 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7650 (tm-30)
REVERT: C  634 GLU cc_start: 0.8555 (tm-30) cc_final: 0.7847 (tm-30)
REVERT: C  669 LYS cc_start: 0.8562 (mtpm) cc_final: 0.7537 (tmtt)
REVERT: C  674 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.8011 (mtp)
REVERT: C  714 GLN cc_start: 0.7815 (mm-40) cc_final: 0.7582 (mm110)
REVERT: D  606 TRP cc_start: 0.6901 (m-10) cc_final: 0.6416 (m-90)
  outliers start: 39
  outliers final: 26
  residues processed: 231
  average time/residue: 0.2638
  time to fit residues: 92.7550
Evaluate side-chains
  227 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 199
  time to evaluate  : 1.852 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  411 ASN
Chi-restraints excluded: chain A residue  447 ASP
Chi-restraints excluded: chain A residue  533 TYR
Chi-restraints excluded: chain A residue  630 VAL
Chi-restraints excluded: chain A residue  649 THR
Chi-restraints excluded: chain A residue  868 ILE
Chi-restraints excluded: chain A residue  936 LEU
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  456 ASP
Chi-restraints excluded: chain B residue  644 GLU
Chi-restraints excluded: chain B residue  681 VAL
Chi-restraints excluded: chain B residue  741 SER
Chi-restraints excluded: chain B residue  785 SER
Chi-restraints excluded: chain B residue  790 SER
Chi-restraints excluded: chain C residue  407 MET
Chi-restraints excluded: chain C residue  447 ASP
Chi-restraints excluded: chain C residue  533 TYR
Chi-restraints excluded: chain C residue  538 VAL
Chi-restraints excluded: chain C residue  630 VAL
Chi-restraints excluded: chain C residue  666 VAL
Chi-restraints excluded: chain C residue  674 MET
Chi-restraints excluded: chain C residue  683 VAL
Chi-restraints excluded: chain C residue  900 CYS
Chi-restraints excluded: chain D residue  445 VAL
Chi-restraints excluded: chain D residue  456 ASP
Chi-restraints excluded: chain D residue  482 THR
Chi-restraints excluded: chain D residue  543 VAL
Chi-restraints excluded: chain D residue  790 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 188 optimal weight:    0.9990
   chunk 114 optimal weight:   10.0000
   chunk 89 optimal weight:    0.8980
   chunk 130 optimal weight:    4.9990
   chunk 197 optimal weight:    5.9990
   chunk 181 optimal weight:    4.9990
   chunk 157 optimal weight:    8.9990
   chunk 16 optimal weight:    9.9990
   chunk 121 optimal weight:    3.9990
   chunk 96 optimal weight:    4.9990
   chunk 124 optimal weight:    0.0030
   overall best weight:    2.1796

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 587 GLN
C 642 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7473
moved from start:          0.5505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056  15978  Z= 0.394
  Angle     :  0.742  15.558  21570  Z= 0.381
  Chirality :  0.047   0.277   2428
  Planarity :  0.006   0.094   2654
  Dihedral  :  5.689  40.566   2152
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  : 11.75 %
    Favored  : 87.95 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 18.80 %
    Favored  : 79.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.67 %
    Twisted General : 0.05 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.60 (0.19), residues: 1966
  helix:  0.46 (0.16), residues: 1058
  sheet: -3.14 (0.37), residues: 152
  loop : -2.87 (0.21), residues: 756

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP D 606 
 HIS   0.004   0.001   HIS B 435 
 PHE   0.029   0.002   PHE B 541 
 TYR   0.018   0.002   TYR A 702 
 ARG   0.009   0.001   ARG D 661 

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3932 Ramachandran restraints generated.
    1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3932 Ramachandran restraints generated.
    1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 210
  time to evaluate  : 1.784 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  414 MET cc_start: 0.7005 (ptp) cc_final: 0.6612 (ptp)
REVERT: A  527 MET cc_start: 0.7323 (ptm) cc_final: 0.5937 (mmt)
REVERT: A  585 MET cc_start: 0.6262 (mmt) cc_final: 0.5896 (mmt)
REVERT: A  599 ARG cc_start: 0.7298 (mtt90) cc_final: 0.7029 (mmt90)
REVERT: A  669 LYS cc_start: 0.8288 (mtpm) cc_final: 0.7458 (tmtt)
REVERT: A  936 LEU cc_start: 0.6046 (OUTLIER) cc_final: 0.5745 (mt)
REVERT: A 1001 TYR cc_start: 0.6000 (p90) cc_final: 0.5721 (p90)
REVERT: B  408 MET cc_start: 0.7353 (mmm) cc_final: 0.7105 (mmt)
REVERT: B  527 MET cc_start: 0.7607 (mtp) cc_final: 0.7083 (mmt)
REVERT: B  601 VAL cc_start: 0.8102 (t) cc_final: 0.7856 (m)
REVERT: C  527 MET cc_start: 0.6679 (ptm) cc_final: 0.5060 (mmt)
REVERT: C  634 GLU cc_start: 0.8597 (tm-30) cc_final: 0.7858 (tm-30)
REVERT: C  669 LYS cc_start: 0.8673 (mtpm) cc_final: 0.7691 (tmtt)
REVERT: C  674 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.8231 (mtp)
REVERT: C  714 GLN cc_start: 0.8009 (mm-40) cc_final: 0.7788 (mm110)
REVERT: C  880 MET cc_start: 0.4005 (mpp) cc_final: 0.3126 (ttm)
REVERT: D  606 TRP cc_start: 0.7289 (m-10) cc_final: 0.6631 (m-90)
  outliers start: 31
  outliers final: 22
  residues processed: 229
  average time/residue: 0.2695
  time to fit residues: 93.2873
Evaluate side-chains
  222 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 198
  time to evaluate  : 1.837 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  411 ASN
Chi-restraints excluded: chain A residue  447 ASP
Chi-restraints excluded: chain A residue  533 TYR
Chi-restraints excluded: chain A residue  630 VAL
Chi-restraints excluded: chain A residue  645 ILE
Chi-restraints excluded: chain A residue  868 ILE
Chi-restraints excluded: chain A residue  936 LEU
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  456 ASP
Chi-restraints excluded: chain B residue  681 VAL
Chi-restraints excluded: chain B residue  741 SER
Chi-restraints excluded: chain B residue  785 SER
Chi-restraints excluded: chain B residue  790 SER
Chi-restraints excluded: chain C residue  533 TYR
Chi-restraints excluded: chain C residue  630 VAL
Chi-restraints excluded: chain C residue  666 VAL
Chi-restraints excluded: chain C residue  674 MET
Chi-restraints excluded: chain C residue  683 VAL
Chi-restraints excluded: chain C residue  900 CYS
Chi-restraints excluded: chain D residue  445 VAL
Chi-restraints excluded: chain D residue  456 ASP
Chi-restraints excluded: chain D residue  482 THR
Chi-restraints excluded: chain D residue  543 VAL
Chi-restraints excluded: chain D residue  790 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 167 optimal weight:    0.9980
   chunk 48 optimal weight:    0.1980
   chunk 144 optimal weight:   30.0000
   chunk 23 optimal weight:    0.0980
   chunk 43 optimal weight:   20.0000
   chunk 157 optimal weight:    5.9990
   chunk 65 optimal weight:    2.9990
   chunk 161 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0370
   chunk 138 optimal weight:    1.9990
   overall best weight:    0.4660

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
C 508 GLN
C 642 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.209339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.182927 restraints weight = 18044.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.174257 restraints weight = 23555.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.170951 restraints weight = 27804.201|
|-----------------------------------------------------------------------------|
r_work (final): 0.3921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7134
moved from start:          0.5607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  15978  Z= 0.178
  Angle     :  0.647  16.650  21570  Z= 0.331
  Chirality :  0.042   0.229   2428
  Planarity :  0.005   0.086   2654
  Dihedral  :  5.367  38.738   2152
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 10.31
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 10.12 %
    Favored  : 89.67 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 19.45 %
    Favored  : 78.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.67 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.22 (0.19), residues: 1966
  helix:  0.88 (0.16), residues: 1054
  sheet: -3.14 (0.37), residues: 152
  loop : -2.82 (0.21), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.001   TRP D 606 
 HIS   0.002   0.001   HIS D 412 
 PHE   0.029   0.001   PHE C1028 
 TYR   0.020   0.001   TYR D 647 
 ARG   0.011   0.000   ARG D 661 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3079.94 seconds
wall clock time: 57 minutes 28.10 seconds (3448.10 seconds total)